Latest ENCODE Research Validates ID Predictions On Non-Coding Repertoire
| September 6, 2012 | Posted by Jonathan M under 'Junk DNA' |
Readers will likely recall the ENCODE project, published in a series of papers in 2007, in which (among other interesting findings) it was discovered that, even though the vast majority of our DNA does not code for proteins, the human genome is nonetheless pervasively transcribed into mRNA. The science media and blogosphere is now abuzz with the latest published research from the ENCODE project, the most recent blow to the “junk DNA” paradigm. Since the majority of the genome being non-functional (as has been claimed by many, including notably Larry Moran, P.Z. Myers, Nick Matzke, Jerry Coyne, Kenneth Miller and Richard Dawkins) would be surprising given the hypothesis of design, ID proponents have long predicted that function will be identified for much of our DNA that was once considered to be useless. In a spectacular vindication of this hypothesis, six papers have been released in Nature, in addition to a further 24 papers in Genome Research and Genome Biology, plus six review articles in The Journal of Biological Chemistry.
The lead publication of the finding (“An Integrated Encyclopaedia of DNA Elements in the Human Genome“) was released in Nature. The abstract reports,
“The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research.” [emphasis added]
They further report that,
“[E]ven using the most conservative estimates, the fraction of bases likely to be involved in direct gene regulation, even though incomplete, is significantly higher than that ascribed to protein- coding exons (1.2%), raising the possibility that more information in the human genome may be important for gene regulation than for biochemical function. Many of the regulatory elements are not constrained across mammalian evolution, which so far has been one of the most reliable indications of an important biochemical event for the organism. Thus, our data provide orthologous indicators for suggesting possible functional elements.”
As this Nature press release states,
“Collectively, the papers describe 1,640 data sets generated across 147 different cell types. Among the many important results there is one that stands out above them all: more than 80% of the human genome’s components have now been assigned at least one biochemical function.” [emphasis added]
The UK Guardian also covered the story, noting that
“For years, the vast stretches of DNA between our 20,000 or so protein-coding genes – more than 98% of the genetic sequence inside each of our cells – was written off as “junk” DNA. Already falling out of favour in recent years, this concept will now, with Encode’s work, be consigned to the history books.” [emphasis added]
This new research places a dagger through the heart of the junk DNA paradigm, and should give adherents to this out-dated assumption yet further cause for caution before they write off DNA, for which function has yet to be identified, as “junk”. Be sure to also check out Casey Luskin’s coverage of the findings at ENV.
68 Responses to Latest ENCODE Research Validates ID Predictions On Non-Coding Repertoire
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Unless you’re a Darwinist.
So what does this mean for modern evolutionary theory? That’s what I want to know. Please post any links that address this question.
For example, isn’t it a claim of modern evolutionary theory that we can reliably determine evolutionary relationships from sections of non-functional DNA precisely because they are non-functional?
(Not to be confused with their “I don’t think an intelligent designer wouldn’t have done it that way, therefore… “argument.”)
A few notes. Here is a neat video on the announcement:
Here is a beaut of a quote on the question of functionality for the remaining remaining 20%:
But it was really not all that hard to see that we are NOT dealing with massive amount of junk in the DNA!
here is physorg’s announcement:
Actually a ‘redefinition of a gene’, despite the denial of Darwinists, was already being forced upon us:
Here is the NY TIMES reporting on ENCODE announcement:
here is science daily’s release:
A few more notes: Here is a bit of history on the Junk DNA argument by evolutionists
more tidbits
Hopefully, one day soon, experts will do a study telling us exactly what ‘quantum computation’ is doing in DNA!
In the following article, Dr. Hameroff expands on the quantum computation aspect of Rieper, Anders and Vedral paper:
Music, video, and Verse:
Well, well, well.
We’ve had several threads over the past few months on this issue, with committed evolutionists proclaiming over and over that junk is pervasive, that the majority of DNA is junk, etc. What say you now? Crickets . . .
Just to toot my own horn for a minute, I have publicly stated on more than one occasion on UD that no more than 5-10% of DNA would ultimately turn out to be non-functional. As far as I know, I haven’t seen anyone else on those threads be willing to make such a concrete assessment. We’re at 80% function now, so it is only a matter of time and a bit more research before we are above 90%.
I would say “Told you so!” but that would be unsporting!
—–
This is a spectacular example of one paradigm making a major prediction and the other paradigm making a major prediction that is exactly the opposite. It is absolutely clear that the evolutionary paradigm has failed miserably and that the design prediction has been borne out.
Will this kill off Darwinian evolution? Of course not. Because it is not based on evidence, but on a philosophical viewpoint. Design is excluded from consideration on philosophical/religious grounds and so the only thing that can be considered is some kind of (unspecified, undefined, unclear) cosmic accident over time.
I can’t wait to hear how this “sheds new light on evolution”. Let the story-telling begin!
Oh, that’s good! Thanks!
A few thoughts after reading the reportage of the literature.
(a) The headline “80%” refers to “some chemical reaction”, and the Morans of this world are poining to a much lower 20% figure for “selectable function”, which is still far higher than expected. The authors, though, defend their terminology on the basis that much genuine function will prove non-selectable, and that one can’t decide something is not useful until you know what it does. So the argument looks more dispassionate if one understands and quotes both figures, since they both do the job of refuting “Junk DNA” (Of course, we all know that no biologist has use that inaccurate term for a DECADE or so. Francis Collins only used it in 2007 for theological reasons
.
(b) If protein-coding genes are now a very small minority of the redefined genes, most of which are non-selectable switches for codong genes shared amongst many species, does population genetics actually mean anything much mathematically now?
(c) If the size of the genome has been swelled to comprise mainly near-neutral elements, does there remain any significant role for natural selection? How can selection handle speciation if speciation is mainly switch configuration?
(d) Much of the extended-genome is not conserved … ie it’s species-specific. What does that do for the rate at which evolution could happen, say between apes and man?
The following ia a quote from Dennis Venema at BioLogos:
“For example, we see the genes for air-based olfaction (smelling) in whales that no longer even have olfactory organs. Humans have the remains of a gene devoted to egg yolk production in our DNA in exactly the place that evolution would predict.”
This is yet another prediction verified for evolution through common ancestry. I know that some on this board are not against evolution or common ancestry so I fail to see why the celebrations. ID proponents are saying this but so do Darwinists. It seems that ID believes it and yet celebrates when there is evidence against it. After all, wasn’t the prediction of pseudo genes a result of evolution through common ancestry? So if this is proof that it may not be the case, isn’t ID refuted too?
I guess what I’m trying to say is that this is just proof to knock of a tip of the evidence iceberg but ID accepts the rest of the iceberg anyway. So what did this accomplish in the end?
Here is a another video announcement of the ENCODE work:
I thought that both air and water are fluids.
I wonder what he thinks the difference is between fluid-based (air) olfaction and fluid-based (water) olfaction.
“Humans have the remains of a gene devoted to egg yolk production in our DNA in exactly the place that evolution would predict.”
Note the ‘would’ predict. I presume he doesn’t have an actual citation of someone predicting that long beforehand. And any instances of confirmed predictions are more a product of luck than any knowledge flowing from evolutionary theory.
What typically happens is that we learn something new in biology that is interpreted in the paradigm of evolutionary thinking. Then if it matches, evolutionists say, “See, that’s what evolution would predict.” If it doesn’t match, the response is that evolution is messy, non-linear, makes changes all the time, and — surprise — that we shouldn’t expect to see the particular feature survive. This kind of illogic has been used over and over.
The simple fact is that evolutionary theory makes very few bona fide predictions. Some things will evolve, some won’t; some features will be preserved, others won’t; some will survive, others won’t. Under the evolutionary paradigm, there is no reason for thinking that any feature of any species will survive through long periods of time. Evolutionary theory can be largely summed up with the following statement: Stuff happens.
@JLAfan2001
In those cases, I would imagine those genes perform more than one function, otherwise they wouldn’t be conserved for tens to hundreds of millions of years. According to wikipedia (typically hostile to our views):
So the “yolk gene” is not a vestigal remnant. According to Whale ‘sense of smell’ revealed, 2010:
Searching for the quote from Dennis Venema leads to Rachel Held Evans blog, which was published over a year after the BBC whale article. Why is he still using that argument?
These developments are deadly to Darwinism (well as a theory it’s already a corpse, but propped up by its supporters despite the stench.)
Kimura said the majority of the genome is selectively neutral. For humans that would mean most of the 4 giga base pairs were not under the influence of selection.
Now that we find most of the 4 giga base pairs are functional, we have to deal with the fact that they are functional without the influence of selection. Hence we find complex features of biology that exist that cannot in principle be attributed to selection. It’s not an argument from igorance, but a proof by contradiction.
to reiterate what Sal has alluded to, non-functional Junk DNA is not so much ‘predicted’ by Darwinism as it is ‘required’ by it. i.e. No Junk, No Darwinism!
Junk DNA Predictions By Leading Evolutionists
A graph featuring ‘Kimura’s Distribution’ being ‘properly used’ is shown in the following video:
At the 2:45 minute mark of the following video, the mathematical roots of the junk DNA argument, that is still used by many Darwinists, can be traced through Haldane, Kimura, and Ohno’s work in the late 1950’s, 60’s through the early 70’s:
Richard Sternberg, who has a PhD. in Evolutionary Biology, traces how the junk DNA argument developed through the mid 1970’s to the early 80’s and beyond in the following article:
Eric Anderson,
Lot’s of evolutionary biologists have given estimates for the amount of junk DNA. I think it’s unlikely that much more than 10% of the genome is functional in meaningful sense, and that’s after reading the ENCODE papers (well, the big ones). Have you read them? Do you understand what the definition of “functional” is for the classes ENCODE uses?
Well wd400 it is a given that natural selection doesn’t do anything in a meaningful sense. Can you reference any evidence that your position’s mechanisms can construct something functional, in a meaningful sense?
But anyway- are there species with little to no junk DNA? Are there varying degrees from “lots” to “zero”? Does “evolution” explain all of that from lots to zero? Then it explains nothing…
Are you sure that ‘functional’ means what you think it means? And, if it does, do you really want to adopt this definition of function consistently in biological discussions?
Mung in #3 asks, “isn’t it a claim of modern evolutionary theory that we can reliably determine evolutionary relationships from sections of non-functional DNA precisely because they are non-functional?”
Neutrally evolving sequences are certainly useful in estimating phylogeny, but ENCODE’s definition tells us nothing about whether sequences are freely accumulating mutations, or if they are tightly constrained by evolution.
Now, every bp in every intron is ‘functional’ under ENCODE’s definition, simply because they are initially transcribed – not because they “do something” for the organism or have any actual biological consequence. This is not what ‘functional’ means to most people (hence the errant claims about the death of junk DNA – again – in the media). ENCODE’s definition of functional tells us exactly nothing about the biological necessity of such sequences or how they evolve, only that on some level they show evidence of biological activity. Hence the bar is very low: ENCODE still only have evidence of function under traditional definitions in 9% of the genome – which is what was predicted long before ENCODE began.
The coordinator of ENCODE has quite a telling discussion about this on his blog.
Joe,
Yeah, actually, evolutionary can explain quite a lot of variation in genome-size and genome-junkiness. Selection is a weaker force in small populations than large ones, since a little extra junk DNA is likely to be nearly-neutral in a small population we can’t control it.
There are many other things that contribute to the junkiness of a genome, and some of them are probable historical accidents. It’s quite an interesting question when you take an evidence-based approach to it – you should try that out.
wd400-
Yeah, it explains everything. even the stuff that surprises the heck out of biologists. BTW evolution is supposedly all historical accidents- nothing was planned.
As for an evidenced-based approach, well that is why I infer Intelligent Design.
paulmc-
Introns ARE functional- ie they do something for the organism- they allow for alternative gene splicing. Take them out and see what happens. And blind and undirected processes can’t account for any level of biological activity. So your position still has some ‘splainin’ to do…
Firstly, a few dozen base pairs are needed for alternative splicing, not entire introns (typical length: 3500 bp). Secondly, few genes reliably produce multiple transcripts, so their introns do not function (except in the ENCODE sense). Thirdly, of those that do produce an additional transcript, an exon is usually skipped – yet a typical human gene has eight introns, meaning most introns are not involved in producing alternative mRNAs even in genes that do exhibit alternative splicing.
Hey paulmc,
Even though I take the ID side, but I wanted to thank you for coming here to engage us in debate. It would be a boring monoculture without dissenting opinions
Paul,
I see what you are saying. And I think it’s probably true. But, do you know what it teaches me? With words like junk be ascribed to “somewhat functional DNA” and function being ascribed to ” somewhat functional DNA” that scientists SUCK at the English language. This is ridiculous, why would ANYONE use the words Junk when it has function? Even if it is a little bit…and why would these scientists use the words “80 percent functional” if it’s not really. Scientists really need some help with their correct word usages. For the commoner like myself, it’s no wonder we have a hard time understanding this kind of literature, it’s just like the news!
On junk-DNA I’ve been called a liar for Jesus by many. 6 September 2012 I can finally say….. I told you so!
paulmc- future uses, as I told you before. As I said you don’t understand how to design and how to design such that you have viable and helpful variation for possible future requirements.
Just because YOU don’t understand the design requirement for introns does not mean there isn’t one.
YOUR position can’t explain introns nor alternative gene splicing. So perhaps you guys should focus on your position for a while, at least until you can get it sorted out.
How many proteins does the human genome produce vs how many genes?
paulmc, good to see you back (and wd400) and to know you are lurking.
So the evolutionary estimate of “real” function is around 10% and my estimate is 90%+. Hmmm . . . The strange thing is that we already know (per your and wd400′s acknowledgement) of about 10% worth of function. So saying that about 10% (plus or minus a couple points) is functional is asserting that we already have figured out essentially all the functional aspects of DNA. Sorry, but that is just laughable. Particularly when we know there are literally thousands of functions that occur in our bodies for which we have not yet identified the source of the information for that function. A fair amount may be epigentic to be sure, but much is likely genetic in origin.
Pervasive, massive quantity junk DNA was more believable and made more sense to the evolutionary story when it just sat there quietly behaving itself and did nothing (you know, the whole “neutral” catch-all idea it was largely based on in the first place). Now we know that the vast majority of DNA is transcribed, so here’s your theory: “At least 70% of the entire genome is transcribed, even though it has no function and is complete junk.” Talk about selection pressure! Not only is DNA awash in junk we are told, but now the cell expends massive resources and energy transcribing 7x more junk than functional strings, and is left to deal with all the transcribed junk literally clogging up the cell. That is a pretty remarkable viewpoint and one that is flatly in opposition to the idea that “conserved stuff is conserved because it has function.”
I know you will stand fast in your belief that DNA is mostly junk, so we probably won’t get anywhere for now. We’ll just keep the friendly bet open. Remember, though, that, by definition, every single discovery of new function moves the needle toward my end of the bet!
as to:
this:
Anyone have any thoughts on this> http://www.genomicron.evolverz.....est-silly/
Anyone have any thoughts on this? (and then you list the onion test)
My thoughts are that human ignorance for why the genomes are the specific varying sizes they are is not a argument for the Darwinian origin of those specific varying sizes! In fact some very credible reasons have been put forth for why it would make ‘engineering sense’ to vary genome sizes as such:
i.e. There is no logical ‘evolutionary progression’ to be found for the amount of DNA in less complex animals to the size of genomes found in more complex animals. In fact the genome sizes are known to vary widely between Kinds/Species despite their differences in complexity and this mystery is known as the c-value enigma:
And yet, even though this C-value enigma is somewhat (very?) paradoxical to the materialistic, neo-Darwinian, point of view, since information is presupposed to simply ‘emerge’ from a material basis and there clearly is no linear correlation to amount of material present and amount of information expressed, from a design point of view we should rightly expect genome sizes to vary within design constraints. Constraints that would obviously be imposed in trying to achieve a ‘optimal design’ for any particular life-form that was designed; For examples of such constraints,,:
As well, at the 7:00 minute mark of this following video, we find that ‘genome length vs. mass’ gives a enigmatic 1/4 power scaling on the plotted graph for a wide range of different creatures. Thus, once again, giving strong indication of a design constraint that was/is imposed, top down, on genome length, and which is inexplicable from the neo-Darwinian framework:
You are all over the place on this one Eric.
Neutral theory was built on observations about polymorphism – not so much function. These precasive RNAs are not conserved (only about 5% of our genome appears to be subject to negative selection).
The idea that selection can get rid of every weakly expensive variant is hyper-selectionist (it’s amusing how Dawkins-like most creationists are when they talk about evolution acutally…). What do you think the cost of one more transcript is? Evolution doesn’t give you a chance to compare a pristine genome with a junky one – just the differences between one genome and another. That’s a recipe for a ratchet that could easily end up with a genome that is complex as in bureaucracy not complex as in a machine.
I just think you have a long way to go form “makes RNA” (as Paul points out that’s every base of every intron!) to “has a function”
wd400 you claim :
No it wasn’t:
So yes, I think wd400 has a point.
…I don’t usually read the BA spam. But even the mutational load argument is about among-species polymorphism (that there are more of them than we’d expect if selectoin was responsible for most changes), not function, which is the error Eric made and I was trying to correct.
In so far that neutral theory has any point worth considering, it is the fact that neutral theory makes it clear that Darwinism is complete pseudo-scientific tripe that refuses to submit to any rigid falsification criteria!
lol. What do you think neutral theory is BA?
as to:
Huge problem, there is no evidence that protein ‘polymorphisms’ are ‘transient’!:
science fiction!
Tell you what wd400, let’s quit playing games and just cut to the chase, and you go ahead and produce actual evidence for Darwinian evolution producing just one molecular machine? I know I will be waiting a long time for you to produce any substantiating evidence, since you have no actual evidence,
and you will try to play stupid games instead of producing actual evidence (because Darwinism is not about what the evidence actually says for you is it?),, but on the other hand I can produce actual evidence of Intelligence producing a molecular machine:
Why do you play games wd400?
I’m not the one playing games. You did whatever it is that you did to create these copy-paste-spam things without even understanding what neutral theory is (as far as I can tell). (Nearly) Neutral theory is pretty relevent to the ENCODE results, so it would be good if you understood it.
wd400:
You’re missing the point. How is it possible that there is so much junk DNA hanging around in our genome for generations? Certainly not because it is being selected for. Instead precisely because, so the thinking goes, it is neutral.
The idea of vast amounts of junk DNA in the genome was at least made more believable and palatable by the idea that it was neutral. As long as it sat there and minded its own business there could be tons of it — the cell wouldn’t care.
Now, however, we know that it doesn’t just sit there. It gets transcribed. Pervasively so. So now we are being asked to believe that the vast majority of the transcription work in the cell (7/8th of the genome), and the subsequent sorting, breakdown and recycling work of all those RNA strands, is utterly, completely, without function and useless. In fact it is much worse than useless. It uses up much of the cell’s transcription and RNA recycling work. I’m certainly not being hyper-selectionist. I have never argued that 100% of DNA has function. No-one is talking about “one more transcript.” We’re talking about the vast majority of the genome.
So are you really going to stick with the position that fully 70% of the genome is transcribed (with all that entails in terms of materials and transcription resources, later sorting and identification of RNA strands, breakdown, etc.), even though it is utterly, completely useless? And that such a massive use of resources would not result in any selection pressure? And that it would not interfere in any way with the small transcribed amount that is functional? Sorry, but that is just laughable.
And based on what evidence? That we haven’t identified a particular function yet? I don’t get it. Even if you don’t accept design, why fight so tooth and nail against the idea of more DNA function? Why not embrace new developments as interesting evidence that might lead us to understand more about how much function DNA really has?
read what I said. You can’t compare a pristine junk-free genome to a very junky one, because evolution would never get that chance.
I don’t really think junk DNA has much to say on design, but I do fight against the sort of mischracterisation of the genome that sees it as a well oiled machine.
So no actual evidence (a molecular machine) to support your position, and then, ironically, right after presenting no actual evidence for your position, you issue a denial that you are playing games! Dog, Tail, Chase! Then after such blatant inanity, you state:
I understand it well enough to know that Dr. Sanford has rigorously shown it to be false.,,, But what I REALLY would like to know is how could you ever truly know if YOU ever understood it to be true if neo-Darwinism were actually true? You simply have no way of establishing 100% certainty in your atheistic/materialistic worldview
wd400:
BA sort of operates in his own sphere. Mostly I am content to just let him do his thing (he’s ID friendly, so am I. I think he’s a believer, so am I – sure, I’ll admit the bias). But sometimes, when scrolling down a page, trying as I might not to wade though all the copy-paste-spam, something catches my eye that makes me say, HUH?
I can’t tell you how long it’s been since I’ve had Kimura’s book in front of me, but that thing about polymorphism’s struck a nerve, so I checked …
How much you want to bet Salvador has even posted on the subject, lol? That’s really testing my memory.
Mung, the point on neutral theory NOT being based on ‘observation of ‘transient’ polymorphisms’ is, as far as I can tell, valid since there is in fact no observational evidence that ‘transient’ proteins exist.
i.e. wd400 claimed:
“Neutral theory was built on observations about polymorphism”
and you cited:
…the neutral theory regards protein and DNA polymorphisms as a transient phase of molecular evolution,,,
,,,Thus since there is no observational evidence of ‘transient polymorphisms’ then the claim is irrelevant, or worse yet, a lie! Moreover, my references from Sanford stand unchallenged even though they should shut the debate down if unchallenged!
BA,
“Transient proteins” and “transient DNA” and “transient polymorphisms” are your own straw-man constructs.
How did Kimura know about polymorphisms, whether in DNA or proteins, without observations?
Why do you place ‘transient polymorphisms’ in quotes? Who are you quoting?
fyi, I do not claim that polymorphisms were the sole basis for the neutral theory. Anyone who has actually read Kimura would know better.
But you completely poo-poo the idea, and you’re wrong. You do no favors for the cause of ID by denying evident facts.
I’ve both defended and criticized Sanford. So what do you hope to gain there?
BA,
This will be my last, but what do you think a “transient” protein is? The transient polymprophisms those profoundly non-Darwinian evolutionary biologists Kimura, Ohto and Nei were talking about were variant that come into a population, stick around and perhaps even fix without having any impact on their hosts survival. There is quite of of evidence that this sort of thing is common.
Um, that’s not what was discovered.
Jonathan M, do you know what mRNA is? Just wondering.
wd400 you claim:
“There is quite (A lot) of evidence that this sort of thing is common.”
really??? you got (a lot) of evidence??? Please do provide a detailed amino acid by amino acid, step by step, ‘trivial’ transition of a single protein to a novel variant.
When Theory and Experiment Collide — April 16th, 2011 by Douglas Axe
Excerpt: Based on our experimental observations and on calculations we made using a published population model [3], we estimated that Darwin’s mechanism would need a truly staggering amount of time—a trillion trillion years or more—to accomplish the seemingly subtle change in enzyme function that we studied.
,,,Mung please cite the actual observational evidence that led Kimura to believe that these DNA and Protein polymorphisms were transient (as you yourself cited!). Myself, regardless of what you personally think of me, I have much observational evidence gathered that argues very strongly for constraint of protein evolvability.
JLAfan says:
Well, I think it is far too early to make that kind of a claim. Let’s wait and see how this all pans out. There is still so much unknown about the genome. It has many more surprises for us.
This result certainly fits with ID much better than with evolution and common descent. For instance, Jonathan M over at Evolution News and Views wrote this in an article stating why this is such a big deal:
Here, courtesy of crev dot info, is a very interesting statement from the article in the Wall St. Journal entitled Junk DNA’ debunked”,
If this is true, wouldn’t you say it has absolutely huge implications for the chimp to man evolutionary story? I mean, come on, we’re talking 30 times more regulatory elements than animals, including chimps! I don’t know what kind of a percentage difference this will turn out to be, but one thing is for sure, it is no where close to the 98% story that evolutionists have been using as evidence to support common descent!
If I am understanding this properly, this would indicate a vast impassable gap between us and chimps, especially given the evolutionary timeline that only allows, what — something like only 6 million years or so for the change from apes to man to have taken place? Simply impossible.
I’ll look forward to the implications of this research as more is learned, evaluated, and published. I think it is going to make the chimp to human idea sound absolutely incredible!
wd400:
I agree with you that both paradigms can accommodate a degree of function and junk. So it is really a question of degree and the overall expectations and weight of the evidence.
That’s OK. I like to fight against the sort of mischaracterization that says a well-oiled system at the macro level can exist and function on the basis of a sea of junk at the micro level.
Now that I think about it, however, such an idea is consistent with the general engineering naivete that characterizes the whole materialist creation story: we have a bunch of chemicals floating around making a mess of things, but voila, out of the chaos emerges life, organisms, functional cellular systems, etc. As long as we don’t ask too many detailed questions about what is really required for a functionally-integrated system to operate, we can cock our head to the side, squint real hard, and kind of imagine that exquisite function ‘just happens’ to emerge from the chaos . . .
wd400:
quoted from crev dot info
Hmm. What evidence would it take to convince you? I think the genome works very much like a well oiled machine! Perhaps it has suffered a little rust over time, but it still works quite well, as the prospering of our race would seem to indicate. Is devolution really evidence against it originally having been an even better well oiled machine? Not in my book. Mutations build up over time, but that is to be expected as natural selection just cannot keep up with them all, especially the ones that are not serious enough to warrant being selected for.
Was it in the original article on Evolution News & Views where they mentioned that even the precise way that DNA folds into a ball and is stored in the cell is important for it’s function? Absolutely amazing. The fold is anything but random and it seems like it would have had to be like that from the beginning.
Dr. Fazale Rana has a short video up on the ENCODE findings:
Here is another video on the ENCODE announcement:
“ENCODE Project Finds Mass Functionality for “Junk” DNA” – podcast
http://intelligentdesign.podom.....0_13-07_00
Jonathan M- Arthur Hunt, #49, is right. Please correct your OP. Just get rid of the “m” of “mRNA” in your first sentence and add an “s” at the end.
And if you want you can put a “x” in front to designate different types of RNAs.
Thank you
tjguy
“If this is true, wouldn’t you say it has absolutely huge implications for the chimp to man evolutionary story? I mean, come on, we’re talking 30 times more regulatory elements than animals, including chimps! I don’t know what kind of a percentage difference this will turn out to be, but one thing is for sure, it is no where close to the 98% story that evolutionists have been using as evidence to support common descent!”
Thank you for sharing this as I think this will prove to be very interesting indeed.
tjguy:
Good point. Yet a thought nags at me. How would you describe the gap without this evidence? Puny, tiny, easily traversible in 6 million years? Or is it sill big, huge, massive, so improbable as to be essentially impossible.
I suppose more evidence will convince a few fence-sitters out there. But the committed materialist is already committed to miracle after miracle just to even get past the laugh test. I’m not sure adding a few more zeroes to the improbabilities will convince anyone who is already avoiding the math.
EA
“I suppose more evidence will convince a few fence-sitters out there. But the committed materialist is already committed to miracle after miracle just to even get past the laugh test. I’m not sure adding a few more zeroes to the improbabilities will convince anyone who is already avoiding the math.”
How true that is
)
Eric said:
Good question. Even if it were 98%, I personally believe it would be essentially impossible by Darwinian means. Even 2% is not pune, tiny, or easily transversible.
I’m a bit confused myself about something. Perhaps someone can help.
When we hear talk of epigenetics, is that the same thing as what the ENCODE project found evidence of or is epigenetics something above and beyond even that?
If I understand it correctly, it is above and beyond even what the ENCODE project found so that would add a whole extra dimension to the differences between apes and humans and further complicate matters – as if it isn’t impossible as it is.
tjguy:
Thanks for your thoughts.
In terms of epigenetics, it is a term that is not used completely consistently, so we have to be careful when we see the term used. In a broad sense, though, it is referring to everything outside of the DNA sequence itself (‘epi’ meaning “upon” or “over,” per my handy dictionary; thus that which is in ‘on top of’ or ‘in addition to’ pure genetic sequence). Sometimes people use the term to describe the higher-level structure of DNA beyond the pure sequence. Other times, they are referring to higher structural elements of the cell/organism completely outside of DNA. There is a whole massive layer of information going on outside of the DNA. I like to keep in mind, for example, that the same DNA exists in cells as diverse as our heart, lungs, eyes, and big toe. Thus, by definition, it is not the DNA that causes different higher level structures.
Indeed, there is a big open question whether all the information for an organism is even contained in the DNA in the first place.
A chicken-and-egg problem . . .
Literally.
It’s remarkable to watch the mental acrobatics take place as committed Darwinists seek to dismiss or minimize the results of the ENCODE project. It’s not as if the results came out of BioComplexity. If Doug Axe or Ann Gauger had published these results, I wouldn’t be surprised to see the dismissal of the findings, as they are on the intellectual blacklist due to their support of ID. Isn’t the ENCODE project the product of hundreds of scientists working nearly a decade, publishing their findings in numerous prestigious peer-reviewed journals (usually the litmus test for what is “scientific”)? What, then, is the problem? This is a striking example of what happens when the Darwinian worldview crashes up against an uncooperative reality. Nick Matzke, paulmc, etc. seem utterly unwilling to discard the hopelessly discredited idea that 90% (or whatever large percentage one may fancy) of the genome is garbage, the leftovers of evolution’s hit-or-miss whimsy. To maintain a semblance of sensibility, such persons have to resort to semantic games (e.g. “what is the definition of functional?”). This a rhetorical strategy that grows evermore hackneyed with each deployment. This same thing happened when ID proponents really started emphasizing the implications of information in DNA. What were previously uncontroversial facts (there’s digital information in DNA, the genetic code is arbitrary, etc. ) were attacked energetically by Darwinists who couldn’t cope with the straightforward inferences that these facts mandated.
ENCODE aside, did it ever really make sense to conclude that most of the genome is nonfunctional? I would contend that it was never really a logical conjecture to make. How on earth could an organism that comprises some 100 trilion cells, exhibits mechanical complexity on both the micro and the macro level, and possesses the most sophisticated computing system in the known universe (i.e. the brain) be derived from a set of blueprints that is mostly junk? Could an automobile be successfully fashioned by such means? A hand calculator? A typewriter? What seems hopelessly absurd in any other context is par for the course in the magnificent neo-Darwinian synthesis.
One last thing – enough with the ‘onion test’! Yes it’s odd, no we have no sure explanation for the present, but nonetheless the default fallback of “look at how weird this is, therefore Darwinian evolution must be the cause” is intellectually lazy and a non-sequitir.
My word Optimus,
Do you know what ENCODE counts as biochemically functional?
Do you realise that non-Darwinian mechanisma are the reason so much of our genome is junk?
Do you have an answer to the onion test? Or can you explain why it’s not relevant?
Well, I read the chief researchers’ comments on the presentation, and I read the main Nature paper, and the big story was “Far more of the non-coding genome has control function than we ever dreamed, and most of the rest (possibly nearly all) has some function, the significance, or not, of which is as yet still unknown.”
So why does all the discussion argue to and from about what is, as yet, unknown, rather than about the highly significant increase in what is known, which flatly contradicts the “junk DNA” hypothesis that only a tiny percentage of introns have “significant” function? That surprise is what the prestigious research team emphasise, and it has many implications worthy of discussion.
The other 60% or whatever will reveal its secrets by and by. Who knows, the bloated nature of the onion genome might even prove to be a rare and instructive example of how the cell’s usually rigorous self-maintenance can fail and accumulate junk. After all, the Elephant Man didn’t demonstrate that all human features are, in reality, tumours.
This is for Eric Anderson’s comment, up in 13.
08 Human vitellogenin psu-gene
http://www.ncbi.nlm.nih.gov/pm.....ool=pubmed
They predicted that there would be remnants of the gene in a particular place on the chromosome, they looked there, and they were there. Is that the sort of thing you had in mind?
wd400:
Yet darwinism did not predict the existence of junk DNA.
And yes the onion test has been answered by more than one person providing more than one answer.
@ wd400
Your comment that non-Darwinian mechanisms account for why so much junk is in the genome simply assumes that which is in doubt. The research done by ENCODE indicates that the genome is not nearly as full of junk as Darwinian zealots would have everyone believe. Regardless of the exact figure they presented, the take-away message (as nicely highlighted by Jon Garvey above) is that way more of the genome is being used than was previously thought. Not only is that significant, but so is the idea that DNA acts in a three-dimensional way that dramatically changes our understanding of how sections of DNA interact with other sections that seem remote (two-dimensionally speaking). I don’t think ENCODE is making the claim that they have elucidated what each and every nucleotide does, but they are giving compelling reason to reject non-function as the starting point.
As far as the onion test is concerned, I already mentioned (reading comprehension helps) that at present there is no sure answer, though, like Joe mentioned, several persons have proposed ideas. My criticism is that it’s a classic argument from ignorance to point to something like the C-value paradox and automatically conclude that it points to a Darwinian origin for DNA generally speaking. That we don’t know why something is as it is does not furnish adequate reason to prefer a cause with unproven explanatory power (Darwinian evolution) over a cause with amply demonstrated explanatory power (ID).